Contacts of the strand formed by residues 483 - 494 (chain C) in PDB entry 5IXM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 483 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C TYR* 3.3 7.3 - - - -
478C ASP* 2.9 32.8 + - + +
481C ALA* 3.9 23.2 - - + +
482C LYS* 1.3 79.6 - - - +
484C PRO* 1.3 73.7 - - + +
508C ILE* 3.3 14.6 - - + +
517C THR* 5.6 1.0 - - - -
518C SER* 2.9 32.4 + - - +
520C TYR* 3.1 22.4 + - - +
71D ARG* 3.7 14.6 - - - +
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Residues in contact with PRO 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C TYR* 3.2 35.0 - - + +
476C TYR 3.6 8.5 - - - +
477C TYR* 3.8 8.5 - - + +
483C GLN* 1.3 88.0 - - + +
485C ALA* 1.3 59.9 + - - +
486C SER* 4.6 6.7 - - - +
487C GLN* 5.1 6.7 - - + +
506C ARG* 4.6 12.6 - - - +
508C ILE* 3.3 4.3 - - - +
520C TYR* 2.7 42.6 + - + +
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Residues in contact with ALA 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C GLN* 4.9 5.8 - - + +
476C TYR* 2.9 19.7 + - + +
477C TYR 5.3 0.2 - - - -
478C ASP* 4.9 11.9 - - + +
483C GLN 3.5 2.6 + - - +
484C PRO* 1.3 73.7 - - - +
486C SER* 1.3 64.5 + - - +
506C ARG 4.8 0.2 - - - -
507C LYS* 3.5 1.0 - - - -
508C ILE* 2.9 38.7 + - + +
520C TYR* 5.2 0.4 - - - -
549C ILE* 3.6 6.2 - - - +
550C LEU* 4.8 3.8 - - + -
69D ILE* 3.7 25.8 - - + -
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Residues in contact with SER 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C ALA* 4.2 2.0 + - - +
475C TYR* 3.6 2.4 - - - -
476C TYR* 2.9 34.8 + - - +
484C PRO* 3.6 2.3 - - - +
485C ALA* 1.3 83.5 - - - +
487C GLN* 1.3 68.1 + - - +
488C LEU* 5.5 2.3 - - - +
505C GLU* 5.5 2.4 - - - +
506C ARG 3.5 8.4 + - - -
507C LYS* 4.3 4.1 - - - +
548C GLY* 5.0 4.5 - - - -
549C ILE* 3.9 29.4 + - - +
550C LEU* 4.3 17.9 + - - +
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Residues in contact with GLN 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C ALA 3.2 6.3 - - - +
475C TYR* 3.9 28.9 - - + -
484C PRO* 5.1 8.7 - - + +
486C SER* 1.3 79.4 + - - +
488C LEU* 1.3 67.2 + - - +
489C VAL* 4.5 17.7 - - + +
504C TYR* 4.6 15.7 - - + -
505C GLU* 3.3 7.1 - - - +
506C ARG* 2.9 53.8 + - + +
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Residues in contact with LEU 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C VAL* 4.3 22.7 - - + -
473C GLY* 3.2 5.7 - - - -
474C ALA* 2.8 55.0 + - + +
486C SER* 5.5 2.5 - - - +
487C GLN* 1.3 79.4 - - - +
489C VAL* 1.3 69.7 + - - +
490C GLY* 5.4 0.2 - - - -
504C TYR* 3.3 9.9 - - - +
505C GLU* 4.5 14.6 - - + +
544C MET* 3.4 31.0 - - + +
545C LEU* 4.6 8.5 - - + +
547C SER* 3.5 11.2 - - - +
548C GLY* 4.4 14.1 - - - +
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Residues in contact with VAL 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C ILE* 5.0 11.7 - - + -
472C VAL 3.6 6.1 - - - +
473C GLY* 4.7 1.3 - - - -
487C GLN* 4.5 19.1 - - + +
488C LEU* 1.3 86.1 - - - +
490C GLY* 1.3 64.3 + - - +
491C LEU* 6.0 2.0 - - + -
503C GLY* 3.4 2.1 - - - -
504C TYR* 2.9 49.0 + - + +
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Residues in contact with GLY 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C ILE* 3.2 12.7 - - - +
472C VAL* 2.8 52.2 + - - +
488C LEU* 5.4 0.4 - - - -
489C VAL* 1.3 78.0 - - - +
491C LEU* 1.3 63.7 + - - -
502C LEU 3.4 9.0 - - - -
503C GLY* 4.3 1.6 - - - -
544C MET* 4.4 4.7 - - - -
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Residues in contact with LEU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469C TRP* 4.1 36.1 - - + -
470C ALA 3.5 4.9 - - - +
471C ILE* 4.1 24.0 - - + -
489C VAL* 6.0 2.9 - - + -
490C GLY* 1.3 82.0 - - - +
492C GLN* 1.3 63.5 + - - +
501C ASN* 3.7 1.4 - - - -
502C LEU* 2.9 54.5 + - + +
544C MET* 4.1 4.6 - - - +
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Residues in contact with GLN 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C ARG 3.9 0.2 - - - +
469C TRP* 3.6 11.0 - - - -
470C ALA* 2.9 41.7 + - + +
491C LEU* 1.3 76.2 - - - +
493C TYR* 1.3 63.9 + - - +
494C ASN* 3.3 24.1 + - - +
499C ALA* 3.9 14.6 - - + +
500C VAL 3.4 6.7 - - - +
501C ASN* 2.6 33.2 + - - +
541C THR* 3.4 40.8 + - + +
544C MET* 4.4 2.5 - - + -
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Residues in contact with TYR 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C ARG* 3.6 5.2 - - + -
469C TRP* 3.3 37.0 - + + +
492C GLN* 1.3 74.7 - - - +
494C ASN* 1.3 73.4 + - - +
495C THR* 3.3 35.9 - - + +
499C ALA* 3.4 1.7 - - - -
500C VAL* 2.9 57.4 + - + +
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Residues in contact with ASN 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ARG* 2.8 50.3 + - + +
469C TRP 5.8 0.2 - - - -
470C ALA* 5.6 1.6 - - - +
492C GLN* 3.3 27.7 + - - +
493C TYR* 1.3 85.0 - - - +
495C THR* 1.3 74.7 + - - +
498C TRP 4.2 8.0 + - - +
499C ALA* 3.9 14.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il